As of Simulink R2019b, there's no way to directly flash an Arduino board using MATLAB/Simulink with ICSP, but there's a workaround that may be suitable.
When you build a model using Simulink, a hex file is generated for AVR targets. This file is generated in the same folder as the model with the same name as model.
For example for arduino_gettingstarted.slx model, a file called arduino_gettingstarted.hex will be generated.
This hex file can be deployed to the target without connecting the USB port.
For example, to deploy the generated file to Arduino Nano using Arduino Uno as ISP, you can run the following command in Windows Command Prompt:
C:\Arduino\R2019b\arduino-1.8.10\hardware\tools\avr/bin/avrdude -CC:\Arduino\R2019b\arduino-1.8.10\hardware\tools\avr/etc/avrdude.conf -v -patmega328p -cstk500v1 -PCOM76 -b19200 -Uflash:w:C:\Users\USERNAME\AppData\Local\Temp\test\arduino_gettingstarted.hex:i
The command above is for example only.
